4UPF | pdb_00004upf

Assembly principles of the unique cage formed by the ATPase RavA hexamer and the lysine decarboxylase LdcI decamer

• PDB DOI: https://doi.org/10.2210/pdb4UPF/pdb
• EM Map EMD-2681: EMDB EMDataResource

• Classification: LYASE/HYDROLASE
• Organism(s): Escherichia coli str. K-12 substr. MG1655
• Expression System: Escherichia coli, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-06-16 Released: 2014-08-20 
• Deposition Author(s): Malet, H., Liu, K., El Bakkouri, M., Chan, S.W.S., Effantin, G., Bacia, M., Houry, W.A., Gutsche, I.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Assembly Principles of a Unique Cage Formed by Hexameric and Decameric E. Coli Proteins.

Malet, H., Liu, K., El Bakkouri, M., Chan, S.W.S., Effantin, G., Bacia, M., Houry, W.A., Gutsche, I.

(2014) Elife 3: 03653

• PubMed: 25097238 
• DOI: https://doi.org/10.7554/eLife.03653
• Primary Citation Related Structures: 
  4UPB, 4UPF


• PubMed Abstract: 
  

  A 3.3 MDa macromolecular cage between two Escherichia coli proteins with seemingly incompatible symmetries-the hexameric AAA+ ATPase RavA and the decameric inducible lysine decarboxylase LdcI-is reconstructed by cryo-electron microscopy to 11 Å resolution. Combined with a 7.5 Å resolution reconstruction of the minimal complex between LdcI and the LdcI-binding domain of RavA, and the previously solved crystal structures of the individual components, this work enables to build a reliable pseudoatomic model of this unusual architecture and to identify conformational rearrangements and specific elements essential for complex formation. The design of the cage created via lateral interactions between five RavA rings is unique for the diverse AAA+ ATPase superfamily.

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Organizational Affiliation: 
• European Molecular Biology Laboratory, Grenoble, France Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, Grenoble, France Unit for Virus Host-Cell Interactions, CNRS, Grenoble, France.
Department of Biochemistry, University of Toronto, Toronto, Canada.
Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, Grenoble, France Unit for Virus Host-Cell Interactions, CNRS, Grenoble, France.
Université Grenoble Alpes, Institut de Biologie Structurale, Grenoble, France Institut de Biologie Structurale, CNRS, Grenoble, France Institut de Biologie Structurale, CEA, Grenoble, France.
Department of Biochemistry, University of Toronto, Toronto, Canada [e-mail].
Unit for Virus Host-Cell Interactions, Université Grenoble Alpes, Grenoble, France Unit for Virus Host-Cell Interactions, CNRS, Grenoble, France [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 93.98 kDa 
• Atom Count: 784 
• Modeled Residue Count: 784 
• Deposited Residue Count: 830 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSINE DECARBOXYLASE, INDUCIBLE	A	715	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  EC: 4.1.1.18
UniProt
Find proteins for P0A9H3 (Escherichia coli (strain K12)) Explore P0A9H3  Go to UniProtKB:  P0A9H3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ATPASE RAVA	B [auth D]	115	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  EC: 3.6.3.1 (PDB Primary Data), 3.6.1 (UniProt)
UniProt
Find proteins for P31473 (Escherichia coli (strain K12)) Explore P31473  Go to UniProtKB:  P31473

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 7.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	EMAN
RECONSTRUCTION	FPM
RECONSTRUCTION	IMAGIC
RECONSTRUCTION	SPIDER

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-08-20 
Deposition Author(s): Malet, H., Liu, K., El Bakkouri, M., Chan, S.W.S., Effantin, G., Bacia, M., Houry, W.A., Gutsche, I.

Revision History  

• Version 1.0: 2014-08-20
  Type: Initial release
  
• Version 1.1: 2014-09-10
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Data collection, Refinement description
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Refinement description